Altered mitochondrial biology and function is considered as an underlying mechanism of burn injury induced hypermetabolism and insulin resistance. Our previous work has characterized a burn mouse model with insulin resistance by in vivo clamp method accompanied with muscle insulin signal proteins in skeletal muscle. The present study aimed at exploring the morphology and functional changes of muscle mitochondrial in this characterized burn animal model. C57BL/6 mice (10–12 weeks) received 30% total body surface area (TBSA) full thickness burn injury or sham burn injury. Gastrocnemius and quadriceps muscles were collected on days 1, 3, and 7 after burn injury. Mitochondrial function was assessed by citrate synthase activity, mitochondrial membrane potential and NAD+/NADH ratio. Gene expression related to mitochondrial biogenesis, dynamics and mitochondrial DNA contents were quantified with real time quantitative PCR. The morphological changes were assessed by a quantitative 2-dimensional transmission electron microscopy (TEM). Our studies demonstrated that the major changes occurred on day 3. Mitochondrial dysfunction was revealed with significantly reduced citrate synthase activity (fig A, B, C), mitochondrial membrane potential and NAD+/NADH ratio. This was accompanied with reduced mitochondrial DNA contents and mRNA expression of cytochrome C (CytC), mitochondrial transcription factor A (TFAM), nuclear respiratory factor 1 (NRF1) and fission protein 1(Fis1) (fig D, E). TEM demonstrated that mitochondria became longer and branched with disrupted cristae as compared to sham burn animals (fig F, G). There was a time dependent reduction to number of cristae time-dependently (fig H). Since CytC is the major component of electron transport chain, NRF1 regulates transcription rregulating cellular growth and nuclear genes required for respiration, heme biosynthesis, and mitochondrial DNA transcription and replication, the latter is also regulated by TFAM and Fis1 is one of the mitochondrial fission factors. We conclude that the above molecular and morphological changes mitochondria are part of the mechanisms of metabolic aberrations caused by burn injury.